To integrate multiple GSEA studies, we propose a hybrid strategy, iGSEA-AT, for choosing random effects (RE) versus fixed effect (FE) models, with an attempt to achieve the potential maximum statistical efficiency as well as stability in performance in various practical situations. In addition to iGSEA-AT, this package also provides options to perform integrative GSEA with testing based on a FE model (iGSEA-FE) and testing based on a RE model (iGSEA-RE). The approaches account for different set sizes when testing a database of gene sets. The function is easy to use, and the three approaches can be applied to both binary and continuous phenotypes.

This package provides a collection of functions for processing and analyzing metabolite data. The namesake function mrbin() converts 1D or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time. The function fia() ranks features according to their impact on classifier models, especially artificial neural network models.

This package implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences (broadly defined). That being said, many of the methods implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a suite of functions for a variety of related topics, such as effect sizes, confidence intervals for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size planning (from the accuracy in parameter estimation (AIPE), power analytic, equivalence, and minimum-risk point estimation perspectives), mediation analysis, various properties of distributions, and a variety of utility functions.

Quantitative methods for benefit-risk analysis help to condense complex decisions into a univariate metric describing the overall benefit relative to risk. One approach is to use the multi-criteria decision analysis framework (MCDA), as in Mussen, Salek, and Walker (2007) <doi:10.1002/pds.1435>. Bayesian benefit-risk analysis incorporates uncertainty through posterior distributions which are inputs to the benefit-risk framework. The brisk package provides functions to assist with Bayesian benefit-risk analyses, such as MCDA. Users input posterior samples, utility functions, weights, and the package outputs quantitative benefit-risk scores. The posterior of the benefit-risk scores for each group can be compared. Some plotting capabilities are also included.

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 <doi:10.1093/bioinformatics/btw098>). It relies on existing simulators for doing the simulation, and currently supports the programs ms', msms and scrm'. It also supports finite-sites mutation models by combining the simulators with the program seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the PopGenome package (<https://github.com/pievos101/PopGenome>).

This package provides a suite of functions for rapid and flexible analysis of codon usage bias. It provides in-depth analysis at the codon level, including relative synonymous codon usage (RSCU), tRNA weight calculations, machine learning predictions for optimal or preferred codons, and visualization of codon-anticodon pairing. Additionally, it can calculate various gene- specific codon indices such as codon adaptation index (CAI), effective number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation index (tAI), mean codon stabilization coefficients (CSCg), and GC contents (GC/GC3s/GC4d). It also supports both standard and non-standard genetic code tables found in NCBI, as well as custom genetic code tables.

It is a novel tool used to identify the candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. (See Gómez-Carballa et al. (2022) <doi: 10.1016/j.envres.2022.112890> and Feng et al. (2022) <doi: 10.7150/ijms.67815> for disease expression profiles; see Wishart et al. (2018) <doi: 10.1093/nar/gkx1037> and Gaulton et al. (2017) <doi: 10.1093/nar/gkw1074> for drug target information; see Kanehisa et al. (2021) <doi: 10.1093/nar/gkaa970> for the details of KEGG database.).

An implementation of multiple-locus association mapping on a genome-wide scale. Eagle can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since Eagle is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. Eagle reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.

Run grass growth simulations using a grass growth model based on ModVege (Jouven, M., P. Carrère, and R. Baumont "Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. Model Description." (2006) <doi:10.1111/j.1365-2494.2006.00515.x>). The implementation in this package contains a few additions to the above cited version of ModVege, such as simulations of management decisions, and influences of snow cover. As such, the model is fit to simulate grass growth in mountainous regions, such as the Swiss Alps. The package also contains routines for calibrating the model and helpful tools for analysing model outputs and performance.

Interface to the HERE REST APIs <https://developer.here.com/develop/rest-apis>: (1) geocode and autosuggest addresses or reverse geocode POIs using the Geocoder API; (2) route directions, travel distance or time matrices and isolines using the Routing', Matrix Routing and Isoline Routing APIs; (3) request real-time traffic flow and incident information from the Traffic API; (4) find request public transport connections and nearby stations from the Public Transit API; (5) request intermodal routes using the Intermodal Routing API; (6) get weather forecasts, reports on current weather conditions, astronomical information and alerts at a specific location from the Destination Weather API. Locations, routes and isolines are returned as sf objects.

This package provides two record linkage data sets on the Italian Survey on Household and Wealth, 2008 and 2010, a sample survey conducted by the Bank of Italy every two years. The 2010 survey covered 13,702 individuals, while the 2008 survey covered 13,734 individuals. The following categorical variables are included in this data set: year of birth, working status, employment status, branch of activity, town size, geographical area of birth, sex, whether or not Italian national, and highest educational level obtained. Unique identifiers are available to assess the accuracy of oneâ s method. Please see Steorts (2015) <DOI:10.1214/15-BA965SI> to find more details about the data set.

This package provides tools for high-dimensional peaks-over-threshold inference and simulation of Brown-Resnick and extremal Student spatial extremal processes. These include optimization routines based on censored likelihood and gradient scoring, and exact simulation algorithms for max-stable and multivariate Pareto distributions based on rejection sampling. Fast multivariate Gaussian and Student distribution functions using separation-of-variable algorithm with quasi Monte Carlo integration are also provided. Key references include de Fondeville and Davison (2018) <doi:10.1093/biomet/asy026>, Thibaud and Opitz (2015) <doi:10.1093/biomet/asv045>, Wadsworth and Tawn (2014) <doi:10.1093/biomet/ast042> and Genz and Bretz (2009) <doi:10.1007/978-3-642-01689-9>.

This package provides a computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..

Machine learning is widely used in information-systems design. Yet, training algorithms on imbalanced datasets may severely affect performance on unseen data. For example, in some cases in healthcare, financial, or internet-security contexts, certain sub-classes are difficult to learn because they are underrepresented in training data. This R package offers a flexible and efficient solution based on a new synthetic average neighborhood sampling algorithm ('SANSA'), which, in contrast to other solutions, introduces a novel â placementâ parameter that can be tuned to adapt to each datasets unique manifestation of the imbalance. More information about the algorithm's parameters can be found at Nasir et al. (2022) <https://murtaza.cc/SANSA/>.

This package provides estimation and inference for while-alive regression models targeting the while-alive loss rate for composite endpoints that include recurrent events and a terminal event. The implementation supports flexible time-varying covariate effects through user-selected time bases, including B-splines, natural splines, M-splines, step functions, truncated linear bases, interval-local bases, and piecewise polynomials. Inference can be performed using cluster-robust variance estimators for cluster-randomized trials, with subject-level (IID) variance as a special case. The package includes prediction and plotting utilities and K-fold cross-validation for selecting basis and tuning parameters. Methodology is based on Fang et al. (2025) <doi:10.1093/biostatistics/kxaf047>.

This package implements convex regression with interpretable sharp partitions (CRISP), which considers the problem of predicting an outcome variable on the basis of two covariates, using an interpretable yet non-additive model. CRISP partitions the covariate space into blocks in a data-adaptive way, and fits a mean model within each block. Unlike other partitioning methods, CRISP is fit using a non-greedy approach by solving a convex optimization problem, resulting in low-variance fits. More details are provided in Petersen, A., Simon, N., and Witten, D. (2016). Convex Regression with Interpretable Sharp Partitions. Journal of Machine Learning Research, 17(94): 1-31 <http://jmlr.org/papers/volume17/15-344/15-344.pdf>.

This package implements contemporaneous Markov chain Monte Carlo (CMCMC) and interchain adaptive Markov chain Monte Carlo (INCA) samplers of Craiu, Rosenthal and Yang (2009) <doi:10.1198/jasa.2009.tm08393> for targets known up to a normalising constant. The samplers run multiple Metropolis chains in parallel and update proposal covariance estimates using contemporaneous particle groups. Built-in target kernels include multivariate normal, logistic regression, Poisson, Gaussian, Gamma, and hierarchical models, with support for user-provided target kernels. The formula interface glm_cmcmc() fits supported generalized linear models using the built-in kernels. CUDA is used when available, and an OpenMP'-enabled CPU backend is available on systems without a CUDA compiler.

Marine fisheries governance and management rely heavily on reliable indicators of stock abundance and fishing pressure to ensure the sustainable utilization of marine resources. Catch Per Unit Effort (CPUE) is widely used as an index of relative abundance, but direct comparison of catch rates is often affected by differences in fishing effort, vessel characteristics, gear efficiency, and operational practices. The FESta package provides methods for fishing effort and CPUE standardization, including vessel-based, gear-based, relative effort, derived effort, generalized linear models, generalized additive models, generalized linear mixed models, ordered quantile transformation models, and multi-gear standardization techniques for fisheries stock assessment and monitoring. To cite our package run this command, citation("FESta").

Computes the test statistic and p-value of the Cramer-von Mises and Anderson-Darling test for some continuous distribution functions proposed by Chen and Balakrishnan (1995) <http://asq.org/qic/display-item/index.html?item=11407>. In addition to our classic distribution functions here, we calculate the Goodness of Fit (GoF) test to dataset which follows the extreme value distribution function, without remembering the formula of distribution/density functions. Calculates the Value at Risk (VaR) and Average VaR are another important risk factors which are estimated by using well-known distribution functions. Pflug and Romisch (2007, ISBN: 9812707409) is a good reference to study the properties of risk measures.

Replacement for nls() tools for working with nonlinear least squares problems. The calling structure is similar to, but much simpler than, that of the nls() function. Moreover, where nls() specifically does NOT deal with small or zero residual problems, nlmrt is quite happy to solve them. It also attempts to be more robust in finding solutions, thereby avoiding singular gradient messages that arise in the Gauss-Newton method within nls(). The Marquardt-Nash approach in nlmrt generally works more reliably to get a solution, though this may be one of a set of possibilities, and may also be statistically unsatisfactory. Added print and summary as of August 28, 2012.

Computes feature-specific R-squared (R2) contributions for boosting tree models using a Shapley-value-based decomposition of the total R-squared in polynomial time. Supports models fitted with XGBoost', LightGBM', and CatBoost', with optimized backend-specific implementations and cached tree summaries suitable for large-scale problems. Multiple visualization tools are included for interpreting and communicating feature contributions. The methodology is described in Jiang, Zhang, and Zhang (2025) <doi:10.48550/arXiv.2407.03515>. Optional CatBoost support uses the R package catboost', which is not distributed on CRAN; installation instructions and released binaries are provided by the CatBoost project at <https://catboost.ai/docs/en/concepts/r-installation>.

This package provides tools to compute and analyze the set of statistically-equivalent (Gaussian, linear) path models which generate the input precision or (partial) correlation matrix. This procedure is useful for understanding how statistical network models such as the Gaussian Graphical Model (GGM) perform as causal discovery tools. The statistical-equivalence set of a given GGM expresses the uncertainty we have about the sign, size and direction of directed relationships based on the weights matrix of the GGM alone. The derivation of the equivalence set and its use for understanding GGMs as causal discovery tools is described by Ryan, O., Bringmann, L.F., & Schuurman, N.K. (2022) <doi: 10.31234/osf.io/ryg69>.

Simulation methods for the Fisher Bingham distribution on the unit sphere, the matrix Bingham distribution on a Grassmann manifold, the matrix Fisher distribution on SO(3), and the bivariate von Mises sine model on the torus. The methods use an acceptance/rejection simulation algorithm for the Bingham distribution and are described fully by Kent, Ganeiber and Mardia (2018) <doi:10.1080/10618600.2017.1390468>. These methods supersede earlier MCMC simulation methods and are more general than earlier simulation methods. The methods can be slower in specific situations where there are existing non-MCMC simulation methods (see Section 8 of Kent, Ganeiber and Mardia (2018) <doi:10.1080/10618600.2017.1390468> for further details).

DVB-T dongles based on the Realtek RTL2832U can be used as a cheap software defined radio, since the chip allows transferring the raw I/Q samples to the host. rtl-sdr provides drivers for this purpose.

The default Linux driver managing DVB-T dongles as TV devices doesn't work for SDR purposes and clashes with this package. Therefore you must prevent the kernel from loading it automatically by adding the following line to your system configuration:

(kernel-arguments '("modprobe.blacklist=dvb_usb_rtl28xxu"))

To install the rtl-sdr udev rules, you must extend 'udev-service-type' with this package. E.g.: (udev-rules-service 'rtl-sdr rtl-sdr)